Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor.
Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor.
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DOI：
10.1093/gbe/evq087
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发表时间：
2011
影响因子：
3.3
通讯作者：
Edwards SV
中科院分区：
文献类型：
--
作者：
Janes DE;Chapus C;Gondo Y;Clayton DF;Sinha S;Blatti CA;Organ CL;Fujita MK;Balakrishnan CN;Edwards SV
基因组的许多非编码区似乎对基因组功能至关重要。大量的非编码序列在哺乳动物中被反复报道，但迄今为止在鸟类和爬行动物中还没有。通过搜索鸡（Gallus gallus）、斑胸草雀（Taeniopygia guttata）和绿色变色龙（Anolis carolinensis）的基因组，我们量化了长保守非编码序列（LCNS）在鸟类和爬行动物之间的保守性，我们将其定义为长度≥500 bp且物种间相似性≥95%的序列。我们发现鸡和斑胸草雀共有4,294个LCNS，两种鸟和Anolis共有574个LCNS。两种鸟类中LCNS组成的基因组百分比（0.0024%）明显高于哺乳动物（<0.0003%至<0.001%），我们发现的差异可能部分由全基因组替换率的差异解释。我们重建了大量的LCNS的祖先（约。8，630），并假设差异损失和大量营业额的这些网站在后裔血统。相比之下，我们估计随着时间的推移，通过获得新的功能来募集LCNS的作用很小。在所有鸟类中，LCNS显著富集了许多发育基因的转录因子结合位点，两种鸟类之间共有的2.9%的LCNS显示出在脑表达序列标签数据库中表达的证据。这些结果表明，保留率的LCNS从哺乳动物和爬行动物（包括鸟类）的祖先不同，这可能反映了不同的角色和基因调控的限制。
Many noncoding regions of genomes appear to be essential to genome function. Conservation of large numbers of noncoding sequences has been reported repeatedly among mammals but not thus far among birds and reptiles. By searching genomes of chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and green anole (Anolis carolinensis), we quantified the conservation among birds and reptiles and across amniotes of long, conserved noncoding sequences (LCNS), which we define as sequences ≥500 bp in length and exhibiting ≥95% similarity between species. We found 4,294 LCNS shared between chicken and zebra finch and 574 LCNS shared by the two birds and Anolis. The percent of genomes comprised by LCNS in the two birds (0.0024%) is notably higher than the percent in mammals (<0.0003% to <0.001%), differences that we show may be explained in part by differences in genome-wide substitution rates. We reconstruct a large number of LCNS for the amniote ancestor (ca. 8,630) and hypothesize differential loss and substantial turnover of these sites in descendent lineages. By contrast, we estimated a small role for recruitment of LCNS via acquisition of novel functions over time. Across amniotes, LCNS are significantly enriched with transcription factor binding sites for many developmental genes, and 2.9% of LCNS shared between the two birds show evidence of expression in brain expressed sequence tag databases. These results show that the rate of retention of LCNS from the amniote ancestor differs between mammals and Reptilia (including birds) and that this may reflect differing roles and constraints in gene regulation.
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影响因子：
14.9
作者：
Abascal F;Zardoya R;Telford MJ
通讯作者：
Telford MJ
影响因子：
4.5
作者：
Kim, Su Yeon;Pritchard, Jonathan K.
通讯作者：
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DOI：
10.1098/rspb.2001.1877
发表时间：
2002-02-07
影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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影响因子：
14.9
作者：
Haider S;Ballester B;Smedley D;Zhang J;Rice P;Kasprzyk A
通讯作者：
Kasprzyk A